CultureMech/.gitignore at main · CultureBotAI/CultureMech · GitHub

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# Python
__pycache__/
*.py[cod]
*$py.class
*.so
.Python
build/
develop-eggs/
dist/
downloads/
eggs/
.eggs/
lib/
lib64/
parts/
sdist/
var/
wheels/
*.egg-info/
.installed.cfg
*.egg

# Virtual environments
venv/
ENV/
env/
.venv

# IDE
.vscode/
.idea/
*.swp
*.swo
*~
.DS_Store

# Testing
.pytest_cache/
.coverage
htmlcov/
.tox/
.mypy_cache/
.dmypy.json
dmypy.json

# Output directories
output/
dashboard/

# OAK cache
.oak_cache/
references_cache/

# UMAP embedding cache (large pickle files - DO NOT commit)
.umap_cache/

# Jupyter
.ipynb_checkpoints/
*.ipynb

# Logs
*.log

# Generated documentation
docs/_build/
docs/schema/

# Temporary files
*.tmp
*.bak
.cache/

# Data layers (see docs/DATA_LAYERS.md)
# Three-tier system: data/raw/ → data/raw_yaml/ → data/normalized_yaml/

# Layer 1: Raw data files (large, can be regenerated or fetched)
data/raw/**/*.json
data/raw/**/*.tsv
data/raw/**/*.csv
data/raw/**/*.tar.gz
data/raw/**/*.zip
data/raw/**/*.html
data/raw/**/*.sql
data/raw/**/.DS_Store

# Keep provenance documentation
!data/raw/**/README.md

# Keep MicrobeMediaParam chemical mappings (essential for CHEBI grounding)
!data/raw/microbe-media-param/compound_mappings_strict_final.tsv
!data/raw/microbe-media-param/compound_mappings_strict_final_hydrate.tsv

# NBRC scraped HTML cache
data/raw/nbrc/scraped/

# Layer 2: Raw YAML (unnormalized, regenerable from data/raw/)
data/raw_yaml/**/*.yaml
data/raw_yaml/**/.DS_Store

# Layer 3: Normalized YAML is VERSION CONTROLLED (curated recipes)
# Keep all data/normalized_yaml/ in git
!data/normalized_yaml/**/*.yaml
data/normalized_yaml/**/.DS_Store

# Processed data (regenerable)
data/processed/
dismech/
data/embeddings/*.tsv.gz

# KG-Microbe data files (too large for GitHub)
data/kgm/merged-kg_edges.tsv
data/kgm/merged-kg_nodes.tsv